Marine sealant will work as well. It's water proof, weather proof, made to adhere to aluminum. Not cheap, but works exceptional well. It's used to seal aquariums, and seems on boats. I use it to seal holes that pierce the hull of the boat, even underwater.
Looks like a great project camper. Could use a few updates while your in there.
I'd find and fix the roof leaks before you fix anything else. No need in fixing the inside if the roof still leaks. Won't take long for all your new work to rot out from water damage. I'd be careful replacing the roof rafters. The roof maybe attached on the top side and that will make replacement a nightmare. You can sister another rafter to the original after you remove all mold, if there is any. Make sure the wood is completely dry before you add another board to the side of it. If not, the new one will rot too. Don't use pressure treated lumber. The chemicals in the treatment will eat the aluminum. You could get by with pressure treated if you use a barrier, like a piece of rubber to keep the pressure treated and aluminum separated. But if you penetrate the rubber seal, you expose the chemicals to the aluminum and introduce corrosion. Only a matter of time before you have a hole.
To find the roof leaks, remove the ceiling, turn on a garden sprinkler and let it saturate the roof. Grab a flashlight and look for leaks inside. Water follows the path of least resistance and the point of entry could be several feet away from where you see the drip. Once you locate the leak, patch the leaky area and run the water test again. I did a water test on my boat. I bought it as a project to rebuild into what I wanted. Stripped to the hull and then set it outside in a rain storm. put the plug in the transom and let if fill up. Crawled underneath the next day and looked for leaks. Found none, drained it, let it dry in the sun for a few days, the commenced the rebuild. You can't test by filling the camper with water, but you can simulate a rain storm. Keep us posted.